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Bioinformatics. 2019 Mar 15;35(6):981-986. doi: 10.1093/bioinformatics/bty713.

Bigmelon: tools for analysing large DNA methylation datasets.

Author information

1
School of Biological Sciences, University of Essex, Colchester, UK.
2
Institute for Social and Economic Research, University of Essex, Colchester, UK.
3
Department of Psychological Sciences, Birkbeck, University of London, London, UK.
4
Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
5
MRC Unit, The Gambia and MRC International Nutrition Group, London School of Hygiene and Tropical Medicine, London, UK.
6
Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
7
University of Exeter Medical School, University of Exeter, Exeter, UK.

Abstract

MOTIVATION:

The datasets generated by DNA methylation analyses are getting bigger. With the release of the HumanMethylationEPIC micro-array and datasets containing thousands of samples, analyses of these large datasets using R are becoming impractical due to large memory requirements. As a result there is an increasing need for computationally efficient methodologies to perform meaningful analysis on high dimensional data.

RESULTS:

Here we introduce the bigmelon R package, which provides a memory efficient workflow that enables users to perform the complex, large scale analyses required in epigenome wide association studies (EWAS) without the need for large RAM. Building on top of the CoreArray Genomic Data Structure file format and libraries packaged in the gdsfmt package, we provide a practical workflow that facilitates the reading-in, preprocessing, quality control and statistical analysis of DNA methylation data.We demonstrate the capabilities of the bigmelon package using a large dataset consisting of 1193 human blood samples from the Understanding Society: UK Household Longitudinal Study, assayed on the EPIC micro-array platform.

AVAILABILITY AND IMPLEMENTATION:

The bigmelon package is available on Bioconductor (http://bioconductor.org/packages/bigmelon/). The Understanding Society dataset is available at https://www.understandingsociety.ac.uk/about/health/data upon request.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

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